Abstract Environmental DNA (eDNA) is increasingly used to measure biodiversity of marine ecosystems. However, key aspects of spatial and temporal dynamics of eDNA remain unknown. Particularly, it is unclear how long eDNA signals persist locally in dynamic marine environments, since degradation rates have predominantly been quantified through mesocosm studies. To determine in situ eDNA residence times, we introduced an eDNA signal from a non-native fish into a Southern California rocky reef ecosystem, and then measured changes in both introduced and background eDNA signals over 96 hours. Foreign eDNA signal could no longer be detected 7.5 hours after introduction, far exceeding disappearance rates quantified in laboratory studies. In addition, native vertebrate eDNA signals varied greatly over the 96 hours of observation, but time of day and tidal direction did not drive this variation in community structure. Species accumulation curves showed that standard sampling protocols using 3 replicate 1 L sea water samples were insufficient to capture full diversity of local marine vertebrates, capturing only 76% of all taxa. Despite this limitation, a single eDNA sample captured greater vertbrate diversity than 18 SCUBA based underwater visual transect surveys conducted at a nearby site. There was no significant difference in species richness between temporal replicates and spatial replicates, suggesting a space for time substitution may be effective for fully capturing the diversity of local marine vertebrate communities in nearshore rocky reef environments. This result is particularly important in designing eDNA metabarcoding sampling protocols to capture local marine species diversity.

Investigating temporal and spatial variation of eDNA in a nearshore rocky reef environment